diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst index cd40828e7d..34d2282312 100755 --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -41,7 +41,7 @@ Syntax * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates * zero or more individual keyword/value pairs may be appended to each react argument -* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* +* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *modify_create* .. parsed-literal:: @@ -55,9 +55,12 @@ Syntax *custom_charges* value = *no* or *fragmentID* no = update all atomic charges (default) fragmentID = ID of molecule fragment whose charges are updated - *modify_create* value = *no* or *fragmentID* - no = use all eligible atoms for create-atoms fit (default) - fragmentID = ID of molecule fragment used for create-atoms fit + *modify_create* keyword values + *fit* value = *all* or *fragmentID* + all = use all eligible atoms for create-atoms fit (default) + fragmentID = ID of molecule fragment used for create-atoms fit + *near* value = R + R = only insert atom/molecule if further than R from existing particles (distance units) Examples """""""" @@ -362,13 +365,23 @@ pre-reaction template. The inserted positions of created atoms are determined by the coordinates of the post-reaction template, after optimal translation and rotation of the post-reaction template to the reaction site (using a fit with atoms that are neither created nor -deleted). Or, the *modify_create* keyword can be used to specify which -post-reaction atoms are used for this fit. The *fragmentID* value must -be the name of a molecule fragment defined in the post-reaction -:doc:`molecule ` template, and only atoms in this fragment -are used for the fit. The velocity of each created atom is initialized -in a random direction with a magnitude calculated from the -instantaneous temperature of the reaction site. +deleted). The *modify_create* keyword can be used to modify the +default behavior when creating atoms. The *modify_create* keyword has +two sub-keywords, *fit* and *near*. One or more of the sub-keywords +may be used after the *modify_create* keyword. The *fit* sub-keyword +can be used to specify which post-reaction atoms are used for the +optimal translation and rotation of the post-reaction template. The +*fragmentID* value of the *fit* sub-keyword must be the name of a +molecule fragment defined in the post-reaction :doc:`molecule +` template, and only atoms in this fragment are used for the +fit. Atoms are created only if no current atom in the simulation is +within a distance R of any created atom, including the effect of +periodic boundary conditions if applicable. R is defined by the *near* +sub-keyword. Note that the default value for R is 0.0, which will +allow atoms to strongly overlap if you are inserting where other atoms +are present. The velocity of each created atom is initialized in a +random direction with a magnitude calculated from the instantaneous +temperature of the reaction site. The handedness of atoms that are chiral centers can be enforced by listing their IDs in the ChiralIDs section. A chiral atom must be